UCL and Sheffield demystify HPC for Biomedical Researchers – winning praise at SC’20

More than 350 people attended the virtual presentation at Supercomputing 2020 featuring the work done in remote training in the QIIME2 application by consortia members, UCL and the University of Sheffield. This project, which took place over a 4-month period with a 6-week live course, introduced medical students into HPC. Led by Andrea Townsend-Nicholson of UCL and Andrew Narracott of the University of Sheffield, the project outcome is a continued evolution of prior courses which were trained at on-site facilities. Out of this work CompBioMed not only has a complete remote course in QIIME2, it also has the nUCLeus cloud HPC education environment, a scalable cluster which is unfederated to a specific cloud platform. This cluster environment, built and managed by Associate Partner Alces Flight, will be positioned for future remote courses in QIIME2 and other, non-compute intensive applications – including forthcoming foundation training in exascale.

The presentation covered everything from moving to remote training, to tuning the cluster environment for QIIME2, to tracking the scaling and spend of the cluster in order to keep future courses affordable and accessible to the consortia. Held in the HPC in Training session during the State of the Practice talks on November 17th this presentation was part of three specially selected projects on novel approaches to HPC education. This talk also included four of the medical students (now first-time authors at SC’20) who worked on the course and on the cluster – allowing the audience to ask candid questions around the real impact of remote compute and scientific training.

This project’s success was thanks to a great team and talented students. Course sponsor Guillaume Hautbergue of the University of Sheffield – HPC Foundation provider David Gregory of UCL – Test, Assessment and Sanity-Checker Marcellus Augustine of UCL – First-time Authors and Participants from the University of Sheffield: Abdullah Ahmad, Joshua Palmer, Ailsa Jones, and Aaisha Sair. Cluster Build & Project Management – Cristin Merritt and Stu Franks of Alces Flight. Finally, we’d like to thank Art Hoti, a Year 4 MSci Biochemistry student at UCL who ran a huge amount of optimisation testing and provided student support to the project leaders Andrea Townsend-Nicholson and Andrew Narracott.

The presentation is now available on YouTube, and can be viewed here: